Comparison of confound adjustment methods in the construction of gene co-expression networks

Adjustment for confounding sources of expression variation is an important preprocessing step in large gene expression studies, but the effect of confound adjustment on co-expression network analysis has not been well-characterized. Here, we demonstrate that the choice of confound adjustment method can have a considerable effect on the architecture of the resulting co-expression network. We compare standard and alternative confound adjustment methods and provide recommendations for their use in the construction of gene co-expression networks from bulk tissue RNA-seq datasets. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02606-0.